Phase separation of ultrathin polymer blend films spun cast onto patterned self-assembled monolayers is examined by atomic force microscopy. Fourier transform analysis of the time evolution of the film topography reveals a coupling between the phase separation process and the surface deformation modes of the blend film. Excitation of these surface modes occurs when the scales of the phase separation coarsening and the deformation modes become commensurate. These excitations decay with time, leading to a structure where only the fundamental mode has appreciable amplitude.